All Published Workflows
17 workflows that have been reviewed and published
Variant calling with OQFE pipeline on cluster systems
This workflow modifies the docker version of the OQFE workflow so that it can be executed on a cluster system using singulari...
This Snakemake pipeline implements the GATK best-practices workflow
This Snakemake pipeline implements the GATK best-practices workflow for calling small germline variants. The usage of thi...
Use an ensemble of variant callers to call variants from ATAC-seq data
A pipeline for running an ensemble of variant callers to predict variants from ATAC-seq reads. The entire pipeline is made up...
A repo for the Twist HiFi capture/snakemake workflow
This is a snakemake workflow for analyzing targeted HiFi sequence datasets. The workflow was designed for Twist gene pane...
MToolBox pipeline written in snakemake to allow a better scalability
This is an work-in-progress update of MToolBox ( PMID:25028726 ). Please find more at the official documentation .
Anlysis of pharmacogenomic targets from Genomic Medicine Swedens heamatology panel.
This workflow is designed to generate sample-specific report with clinical guidelines dependent on variants detected in a Gen...
Perform error-prone data preparation for whole genome regression modeling
An awesome whole genome regression modeling pipeline
This is the home of the pipeline, istari. Its long-term goals: ...
Genetic pipeline to detect variants from a genome of reference
Genetic pipeline inspired by Google's DeepVariant in order to detect cancer-causing alleles. Snakemake workflow, CNN with Ker...
Genome-to-genome analysis reveals associations between human and mycobacterial genetic variation in tuberculosis patients from Tanzania
Preprint: https://doi.org/10.1101/2023.05.11.23289848 Full summary statistics: https://doi.org/10.5281/zenodo.6373034 Reporte...
A pipeline for multi-trait genome-wide association studies (GWAS) using MANTA
A pipeline for multi-trait genome-wide association studies (GWAS) using MANTA . A method for joint analysis of summary st...
GermlineStructuralV-nf: Comprehensive Structural Variant Identification Pipeline for Human Genome Using Multi-Caller Approach
GermlineStructuralV-nf GermlineStructuralV-nf is a pipeline for identifying structural variant events in human Illumina short...